PDBStrand (cdk 2.9 API)

java.lang.Object
- org.openscience.cdk.ChemObject
- - org.openscience.cdk.AtomContainer
  - - org.openscience.cdk.Strand
    - - org.openscience.cdk.protein.data.PDBStrand

All Implemented Interfaces:

Serializable, Cloneable, IAtomContainer, ICDKObject, IChemObject, IChemObjectListener, IStrand
```
public class PDBStrand
extends Strand
```
An entry in the PDB database. It is not just a regular protein, but the regular PDB mix of protein or protein complexes, ligands, water molecules and other species.

Author:

Egon Willighagen

See Also:

Serialized Form

Source code:
main

Belongs to CDK module:
pdb

Keywords:

polymer

Created on:

2006-04-19

Field Summary
- Fields inherited from class org.openscience.cdk.AtomContainer
  atomCount, atoms, bondCount, bonds, growArraySize, lonePairCount, lonePairs, singleElectronCount, singleElectrons, stereoElements

Constructor Summary

Constructors
Constructor Description

PDBStrand()
Constructs a new Polymer to store the Monomers.

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`void`	`addAtom(IAtom oAtom, IMonomer oMonomer)`	Adds the atom oAtom to a specified Monomer.
`Collection<String>`	`getMonomerNamesInSequentialOrder()`	Returns the monomer names in the order in which they were added.
`String`	`toString()`	Returns a one line description of this IChemObject.

Methods inherited from class org.openscience.cdk.Strand
addAtom, clone, getMonomer, getMonomerCount, getMonomerNames, getMonomers, getStrandName, getStrandType, removeMonomer, setStrandName, setStrandType

Methods inherited from class org.openscience.cdk.AtomContainer
add, addBond, addBond, addBond, addElectronContainer, addLonePair, addLonePair, addSingleElectron, addSingleElectron, addStereoElement, atoms, bonds, contains, contains, contains, contains, contains, electronContainers, getAtom, getAtomCount, getAtomNumber, getBond, getBond, getBondCount, getBondNumber, getBondNumber, getBondOrderSum, getConnectedAtomsCount, getConnectedAtomsList, getConnectedBondsCount, getConnectedBondsCount, getConnectedBondsList, getConnectedElectronContainersList, getConnectedLonePairsCount, getConnectedLonePairsList, getConnectedSingleElectronsCount, getConnectedSingleElectronsList, getElectronContainer, getElectronContainerCount, getFirstAtom, getLastAtom, getLonePair, getLonePairCount, getLonePairNumber, getMaximumBondOrder, getMinimumBondOrder, getSingleElectron, getSingleElectronCount, getSingleElectronNumber, getTitle, indexOf, indexOf, indexOf, indexOf, isEmpty, lonePairs, remove, removeAllBonds, removeAllElectronContainers, removeAllElements, removeAtom, removeAtom, removeAtomAndConnectedElectronContainers, removeAtomOnly, removeAtomOnly, removeBond, removeBond, removeBond, removeElectronContainer, removeElectronContainer, removeLonePair, removeLonePair, removeSingleElectron, removeSingleElectron, setAtom, setAtoms, setBonds, setStereoElements, setTitle, singleElectrons, stateChanged, stereoElements

Methods inherited from class org.openscience.cdk.ChemObject
addListener, addProperties, compare, getBuilder, getFlag, getFlags, getFlagValue, getID, getListenerCount, getNotification, getProperties, getProperty, getProperty, notifyChanged, notifyChanged, removeListener, removeProperty, setFlag, setFlags, setID, setNotification, setProperties, setProperty, shallowCopy

Methods inherited from class java.lang.Object
equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Methods inherited from interface org.openscience.cdk.interfaces.IAtomContainer
add, addBond, addBond, addBond, addElectronContainer, addLonePair, addLonePair, addSingleElectron, addSingleElectron, addStereoElement, atoms, bonds, contains, contains, contains, contains, contains, electronContainers, getAtom, getAtomCount, getAtomNumber, getBond, getBond, getBondCount, getBondNumber, getBondNumber, getBondOrderSum, getConnectedAtomsCount, getConnectedAtomsList, getConnectedBondsCount, getConnectedBondsCount, getConnectedBondsList, getConnectedElectronContainersList, getConnectedLonePairsCount, getConnectedLonePairsList, getConnectedSingleElectronsCount, getConnectedSingleElectronsList, getElectronContainer, getElectronContainerCount, getFirstAtom, getLastAtom, getLonePair, getLonePairCount, getLonePairNumber, getMaximumBondOrder, getMinimumBondOrder, getSingleElectron, getSingleElectronCount, getSingleElectronNumber, getTitle, indexOf, indexOf, indexOf, indexOf, isEmpty, lonePairs, remove, removeAllBonds, removeAllElectronContainers, removeAllElements, removeAtom, removeAtom, removeAtomAndConnectedElectronContainers, removeAtomOnly, removeAtomOnly, removeBond, removeBond, removeBond, removeElectronContainer, removeElectronContainer, removeLonePair, removeLonePair, removeSingleElectron, removeSingleElectron, setAtom, setAtoms, setBonds, setStereoElements, setTitle, singleElectrons, stereoElements

Methods inherited from interface org.openscience.cdk.interfaces.ICDKObject
getBuilder

Methods inherited from interface org.openscience.cdk.interfaces.IChemObject
addListener, addProperties, getFlag, getFlags, getFlagValue, getID, getListenerCount, getNotification, getProperties, getProperty, getProperty, notifyChanged, notifyChanged, removeListener, removeProperty, setFlag, setFlags, setID, setNotification, setProperties, setProperty

Methods inherited from interface org.openscience.cdk.interfaces.IChemObjectListener
stateChanged

- Constructor Detail
  - PDBStrand
```
public PDBStrand()
```
    Constructs a new Polymer to store the Monomers.
- Method Detail
  - addAtom
```
public void addAtom(IAtom oAtom,
                    IMonomer oMonomer)
```
    Adds the atom oAtom to a specified Monomer. Additionally, it keeps record of the iCode.
    
    Specified by:
    
    addAtom in interface IStrand
    
    Overrides:
    
    addAtom in class Strand
    
    Parameters:
    
    oAtom - The atom to add
    
    oMonomer - The monomer the atom belongs to
  - getMonomerNamesInSequentialOrder
```
public Collection<String> getMonomerNamesInSequentialOrder()
```
    Returns the monomer names in the order in which they were added.
    
    See Also:
    
    IPolymer.getMonomerNames()
  - toString
```
public String toString()
```
    Description copied from class: AtomContainer
    
    Returns a one line description of this IChemObject.
    
    Specified by:
    
    toString in interface IChemObject
    
    Overrides:
    
    toString in class Strand
    
    Returns:
    
    a String representation of this object